Systems and methods for mechanosynthesis

ABSTRACT

Systems and methods for mechanosynthesis including those that avoid the need for a bootstrap process, avoid the need to build tips via mechanosynthesis, avoid the need for charging tips with feedstock during a build sequence, avoid the need to dispose of reaction byproducts, reduce the design complexity of new tips, and reduce or avoid the need for multiple positional means or tip switching.

CROSS-REFERENCE TO RELATED APPLICATIONS

Not applicable.

FEDERALLY SPONSORED RESEARCH

Not applicable.

SEQUENCE LISTING OR PROGRAM

Not applicable.

FIELD OF INVENTION

The present invention is directed to systems and methods that performmechanosynthesis, including the use of modular tips and tips bound to asurface.

BACKGROUND OF THE INVENTION

Scanning Probe Microscopes (SPM, including e.g., AFM, SFM, and STM) havelong been used, in conjunction with ultra-sharp tips, to move individualatoms or molecules to precise locations. When such site-specificpositioning (and force, if necessary) is used to make or break chemicalbonds, this is referred to as mechanosynthesis. (Oyabu, Custance et al.,“Mechanical vertical manipulation of selected single atoms by softnanoindentation using near contact atomic force microscopy,” Phys. Rev.Lett., 17, 2003; Morita, Sugimoto et al., “Atom-selective imaging andmechanical atom manipulation using the non-contact atomic forcemicroscope,” J. Electron Microsc., 2, 2004; Oyabu, Custance et al.,“Mechanical Vertical Manipulation of Single Atoms on the Ge(111)-c(2×8)Surface by Noncontact Atomic Force Microscopy,” Seventh InternationalConference on non-contact Atomic Force Microscopy, Seattle, Wash., 2004;Sugimoto, Jelinek et al., “Mechanism for Room-Temperature Single-AtomLateral Manipulations on Semiconductors using Dynamic Force Microscopy,”Physical Review Letters, 10, 2007; Sugimoto, Pou et al., “ComplexPatterning by Vertical Interchange Atom Manipulation Using Atomic ForceMicroscopy,” Science, 2008).

Conceptually, mechanosynthesis might be broken into several components:A source of atoms or molecules (“feedstock”) used to build (includingmodifying) workpieces; a place where feedstock is stored while awaitinguse (a “feedstock depot”); the product being built (a “workpiece”); aplace to store reaction byproducts (a “trash depot”); a structure thatdirectly performs mechanosynthesis reactions (a “tip”); a surface (or“presentation surface”), which can serve several purposes includingserving as a feedstock depot and a surface upon which to build theworkpiece; and a positional means (e.g., an SPM probe) which controlsthe relative position of, e.g., tips and workpieces, to facilitate thedesired reactions.

Not all systems will have each of these parts as discrete entities, andsome will be missing completely. For example, in some mechanosynthesisexperiments, one atom was interchanged for another on a surface. In suchcases, the presentation surface, feedstock depot, and workpiece were oneand the same. In this work, there was no trash depot, since there wereno reaction byproducts. Also, note that in some previous examples ofsuch work, only one tip was required because only one or two distinctreactions were being performed (although they may have occurred manytimes each), and one tip sufficed for all reactions.

However, as the desired reactions become more varied, greaterflexibility can be obtained by having a distinct feedstock, feedstockdepot, trash depot, presentation surface, and workpiece. Also, multipletips may be required, each designed to facilitate a particular reactionor set of reactions. Note that a requirement for multiple tips impliessome way to bring multiple tips to bear for sequential or paralleloperation (e.g., multiple positional means, or some way to swap tips ona single positional means).

As an example of systems that use discrete feedstock, feedstock depots,presentation surfaces, workpieces, and multiple tips, among otherpossible components, methods for the creation of atomically-precise tipsfrom non-atomically-precise tips (“bootstrapping”) have been described,along with numerous mechanosynthetic reactions which employ a variety oftips, and methods for using multiple reactions to form build sequencesfor creating complex workpieces (e.g., see patent documents U.S. Pat.No. 9,244,097, US Patent Publication No. 20150355228, US PatentPublication No. 20130184461, US Patent Publication No. 20130178627, USPatent Publication No. 20130178626, U.S. Pat. No. 8,276,211, and U.S.Pat. No. 8,171,568).

Systems capable of more varied build sequences tend to have higherchemical and equipment complexity. For example, chemically,bootstrapping is not a simple process. Neither is the design of newtips, along with the reactions to regenerate tips which are to be usedmultiple times. Further, feedstock needs to be provided in achemically-appropriate manner (e.g., feedstock needs to be provided in amanner that will not allow it to react inappropriately with itself,other feedstock, the feedstock depot, or in ways counter to itsdesignated tip binding modes).

In terms of equipment, a larger number of reactions, more types offeedstock, and larger workpieces can all require a larger presentationsurface. A larger presentation surface means that the positional meansmust maintain sub-Angstrom accuracy over longer distances. Additionally,if multiple tips are required, some solution to the problem of usingeach tip as needed must be provided.

The chemical problems can and have been addressed, as shown by the citedreferences. And, the equipment problems can all be addressed.

For example, while obtaining the requisite accuracy can be challenging,it is by no means infeasible. Software can be used to enhance thepositional accuracy of mechanosynthesis equipment either by correctingfor various types of positional errors (Ceria, Ducourtieux et al.,“Estimation of the measurement uncertainty of LNE's metrological AtomicForce Microscope using virtual instrument modeling and Monte CarloMethod,” 2015) or through the use of image recognition, allowing thelocation of a tip to be determined based on the observed surfacefeatures. (Lapshin, “Feature-oriented scanning methodology for probemicroscopy and nanotechnology,” Nanotechnology, 9, 2004; “Automaticdrift elimination in probe microscope images based on techniques ofcounter-scanning and topography feature recognition,” MeasurementScience and Technology, 3, 2007; “Feature-Oriented Scanning ProbeMicroscopy,” Encyclopedia of Nanoscience and Nanotechnology, 2011;Celotta, Balakirsky et al., “Invited Article: Autonomous assembly ofatomically perfect nanostructures using a scanning tunnelingmicroscope,” Rev Sci Instrum, 12, 2014)

Hardware can also be used to refine microscope tip position. Manymicroscope systems are open-loop, meaning they do not employ metrologyto correct tip position. However, closed-loop systems which do employmetrology are available. For example, AttoCube's (attocube systems AG,Muenchen, Germany) attoDRY LAB claims <1 nm sensor resolution with nopiezo hysteresis, attained using interferometry. And, multi-tip systemsare also available. And, in addition to literature describing the customfabrication of multi-probe SPMs (Eder, Kotakoski et al., “Probing fromboth sides: reshaping the graphene landscape via face-to-face dual-probemicroscopy,” Nano Letters, 5, 2013), various vendors sell systems thathave either more than one probe, or the ability to swap tips on a singleprobe. For example, the MultiView 4000 (NANONICS IMAGING LTD.HEADQUARTERS, Israel), which can employ up to 4 probes, the “Titanium”(NT-MDT Co., Building 100, Zelenograd, Moscow 124482, Russia), which hasa cartridge that can automatically swap between 38 probes, and the LTQuadraProbe™ (RHK Technology, Inc, Troy, Mich. 48083 USA) which includes4 probes.

However, even though the chemical and equipment challenges inherent incomplex mechanosynthesis can be solved, the solutions can increase thecost and complexity of the systems, slow their functioning, and increasethe difficulty of designing and manufacturing new tips, reactions, andbuild sequences. Other solutions, including simply avoiding some of theproblems in the first place, would therefore be useful.

BRIEF SUMMARY OF THE INVENTION

The present invention is directed to systems, methods, and products forthe fabrication of atomically-precise tips used for mechanosynthesis,provisioning such tips in a manner which increases the efficiency ofmechanosynthesis, and provides a novel design paradigm for the creationof new tips. Aspects of the invention also allow for reduced hardwareand software complexity, and positional means optimized formechanosynthesis.

BRIEF DESCRIPTION OF DRAWINGS

For a more complete understanding of the present invention, reference isnow made to the following descriptions taken in conjunction with theaccompanying drawings, in which:

FIG. 1 depicts the modular parts of an exemplary tip.

FIG. 2 depicts the modular parts of another exemplary tip.

FIG. 3 depicts the AbstractO tip surface-mounted on Silicon.

FIG. 4 depicts the HDonationO tip surface-mounted on Silicon.

FIG. 5 depicts the C2DonationO tip surface-mounted on Silicon.

FIG. 6 depicts the MeDonationO tip surface-mounted on Silicon.

FIG. 7 depicts a tip surface-mounted on Silicon which can beSiH3DonationO, GeH3DonationO, SiMe3DonationO or GeMe3DonationO.

FIG. 8 depicts the AbstractNH tip surface-mounted on Silicon.

FIG. 9 depicts the HDonationNH tip surface-mounted on Silicon.

FIG. 10 depicts the C2DonationNH tip surface-mounted on Silicon.

FIG. 11 depicts the MeDonationNH tip surface-mounted on Silicon.

FIG. 12 depicts a tip surface-mounted on Silicon which can beSiH3DonationNH, GeH3DonationNH, SiMe3DonationNH or GeMe3DonationNH.

FIG. 13 depicts the AbstractS tip surface-mounted on Gold.

FIG. 14 depicts the HDonationS tip surface-mounted on Gold.

FIG. 15 depicts the C2DonationS tip surface-mounted on Gold.

FIG. 16 depicts the MeDonationS tip surface-mounted on Gold.

FIG. 17 depicts a tip surface-mounted on Silicon which can beSiH3DonationS, GeH3DonationS, SiMe3DonationS or GeMe3DonationS.

FIG. 18 depicts a synthetic route for the AbstractO tip.

FIG. 19 depicts a synthetic route for the HDonationO tip.

FIG. 20 depicts a synthetic route for the C2DonationO tip.

FIG. 21 depicts a synthetic route for the MeDonationO tip.

FIG. 22 depicts a synthetic route for the SiH3DonationO tip.

FIG. 23 depicts a synthetic route for the GeH3DonationO tip.

FIG. 24 depicts a synthetic route for the SiMe3DonationO tip.

FIG. 25 depicts a synthetic route for the GeMe3DonationO tip.

FIG. 26 depicts a synthetic route for the AbstractNH tip.

FIG. 27 depicts a synthetic route for the HDonationO tip.

FIG. 28 depicts a synthetic route for the C2DonationO tip.

FIG. 29 depicts a synthetic route for the MeDonationO tip.

FIG. 30 depicts a synthetic route for the SiH3DonationO tip.

FIG. 31 depicts a synthetic route for the GeH3DonationO tip.

FIG. 32 depicts a synthetic route for the SiMe3DonationO tip.

FIG. 33 depicts a synthetic route for the GeMe3DonationO tip.

FIG. 34 depicts a synthetic route for the AbstractS tip.

FIG. 35 depicts a synthetic route for the HDonationS tip.

FIG. 36 depicts a synthetic route for the C2DonationS tip.

FIG. 37 depicts a synthetic route for the MeDonationS tip.

FIG. 38 depicts a synthetic route for the SiH3DonationS tip.

FIG. 39 depicts a synthetic route for the GeH3DonationS tip.

FIG. 40 depicts a synthetic route for the SiMe3DonationS tip.

FIG. 41 depicts a synthetic route for the GeMe3DonationS tip.

FIG. 42 depicts a synthetic route for the FHD-104X intermediate.

FIG. 43 depicts a synthetic route for the NHD-103X intermediate.

FIG. 44 depicts photo-activation of a halogen-capped tip.

FIG. 45 depicts photo-activation of a Barton ester-capped tip.

FIG. 46 depicts an exemplary synthesis of a tip with Barton ester cap.

FIG. 47 depicts the use of surface-mounted tips where the workpiecemoves.

FIG. 48 depicts the use of surface-mounted tips where the surface moves.

FIG. 49 depicts a metrology setup for measuring six degrees of freedom.

DETAILED DESCRIPTION OF THE INVENTION Definitions

The following definitions are used herein:

An “adamantane” molecule comprises a 3D cage structure of ten carbonatoms, each terminated with one or two hydrogen atoms, having thechemical formula C10H16 and representing the smallest possible unit cageof crystalline diamond.

An “adamantane-like” structures include one or more adamantanes, one ormore adamantanes where one or more atoms have been substituted withatoms or molecular fragments of like or similar valence, including e.g.,Nitrogen, Oxygen, and Sulfur-substituted variations, and similarmolecules comprising polycyclic or cage-like structures. By way ofexample, and not of limitation, adamantane-like structures would includeadamantane, heteroadamantanes, polymantanes, lonsdaleite, crystallinesilicon or germanium, and versions of each of the foregoing where, forexample, Fluorine is used for termination instead of Hydrogen, or wheretermination is incomplete.

An “atom” includes the standard use of the term, including a radical,which, for example, may be just a proton in the case of H⁺.

“Atomically-precise” means where the position and identity of each atomis known to a precision adequate to enable a site-specificmechanosynthetic reaction.

The “bridgehead” position in an adamantane-like molecular structurerefers to a structural atom that is bonded to three other structuralatoms and may be terminated by one or more nonstructural atoms. This iscontrasted with a “sidewall” position which refers to a structural atomthat is bonded to two other structural atoms and is terminated by one ormore nonstructural atoms.

A “build sequence” is one or more mechanosynthetic reactions arranged inan ordered sequence that permits the assembly, disassembly, ormodification of a workpiece.

A “chemical bond” is an interatomic covalent bond, an interatomic ionicbond, or interatomic coordination bond, as these terms are commonlyunderstood by practitioners skilled in the art.

A “chemical reaction” is said to occur when chemical bonds are formed,broken, or altered.

“Diamond” is a crystal of repeating adamantane cage units arranged invarious well-known crystallographic lattice geometries.

“Diamondoid” materials include any stiff covalent solid that is similarto diamond in strength, chemical inertness, or other important materialproperties, and possesses a three-dimensional network of bonds. Examplesof such materials include but are not limited to (1) diamond, includingcubic and hexagonal lattices and all primary and vicinalcrystallographic surfaces thereof, (2) carbon nanotubes, fullerenes, andother graphene structures, (3) several strong covalent ceramics of whichsilicon carbide, silicon nitride, and boron nitride are representative,(4) a few very stiff ionic ceramics of which sapphire (monocrystallinealuminum oxide) is representative, and (5) partially substitutedvariants of the above that are well-known to those skilled in the art.

“Feedstock” is the supply of atoms used to perform mechanosyntheticreactions on a workpiece. Feedstock may take the form of an atom oratoms (a group or molecule), including radicals (e.g., .GeH2, .CH2).

A “handle structure” comprises a plurality of atoms whose bondingpattern is not altered during a site-specific mechanosynthetic chemicalreaction and whose primary function is to hold a tip(s) or workpiece(s)to facilitate a mechanosynthetic chemical reaction to when the handlestructure is manipulated by a positional device. Handle structure mayinclude the null case.

An “inert environment” includes, but is not limited to, UHV, helium,neon, or other noble gases either individually or in combination, orother gases or liquids that do not react with the tip, feedstock, orworkpiece during mechanosynthetic operations.

“Inverted mode” is the strategy of performing mechanosynthesis by movingthe workpiece to the appropriate tip, rather than the “conventionalmode” of moving a tip to a stationary workpiece.

“Mechanical force” may include applied mechanical forces havingpositive, negative, or zero magnitude. Chemical reactions driven by theapplication of mechanical force include reactions that are (1) driventhrough its reaction barrier by mechanically forcing reactants orproducts through the transition state, or (2) driven away from anundesired reaction by mechanically restraining potentially reactivesites from attaining closer physical proximity, or (3) allowed to occurby bringing potentially reactive sites into closer physical proximitywhen zero mechanical force is required to do so, as for example when noreaction barrier exists.

“Mechanosynthesis” is the use of positional control and mechanical forceto facilitate one or more site-specific chemical reactions involved inthe creation of a workpiece. The use of voltage biases combined withmechanical force-based mechanosynthesis is not required, but is includedin the definition of mechanosynthesis.

A “mechanosynthetic reaction” (sometimes referred to as a “reaction”when context makes it clear that the reaction is mechanosynthetic) is achemical reaction carried out using mechanosynthesis.

A “meta-tip” is a tool to which multiple tips are attached. For example,a meta-tip could be prepared using a conventional SPM probe with a flatsurface on the end, which is then functionalized with the desired tips.

A “modular tip” is a synthetic tip with a modular design, where modulesinclude an active site, a body, and legs (which may have linkers). Tipsfor donation reactions may also have a feedstock module. A modular tipmay be referred to as simply a “tip” when context makes the type of tipclear.

A “positional device” is a device capable of exerting atomically-precisepositional control on a mechanosynthetic tip, tool, or workpiece, andmay include, but is not limited to, scanning probe microscopes (SPM) andatomic force microscopes (AFM) and related devices, a miniaturized orMEMS-scale SPM or AFM, a robotic arm mechanism of any size scale, orother appropriate manipulation system capable of atomically-precisepositional control and appropriate force application.

A “presentation surface” is a surface which can be used for, among otherpurposes, binding tips for use in mechanosynthesis, and as a base onwhich to build a workpiece. Although generally monolithic, there is noreason a presentation surface cannot be composed of more than onematerial (e.g., gold and silicon could both be used where each hasadvantageous aspects), or composed of multiple non-adjacent surfaces.May be referred to simply as a “surface” when context makes the meaningclear. Presentation surfaces include the appropriate areas on meta-tips.

“Site-specific” refers to knowing, and being able to constrain, with adesired degree of reliability, the position at which a mechanosyntheticreaction takes place.

A “structural atom” in an adamantane-like molecular structure refers toan atom comprising the cage framework, for example a carbon atom in anadamantane molecule. More generally, a structural atom is an atom thatcomprises part of the backbone or overall structure in a highly-bondedmolecule.

A “synthetic tip” is an atomically-precise tip manufactured via a bulkmethod, such as gas or solution-phase chemistry, rather than viamechanosynthesis. May be referred to as simply a “tip” when contextmakes the type of tip clear.

A “terminating atom” refers to an atom that does not serve as astructural atom but absorbs unused valences of a structural atom. Forexample, a hydrogen atom in an adamantane molecule.

A “three-dimensional” workpiece means a workpiece including a lattice ofatoms whose covalent structure occupies three dimensions, consideringatoms as points, and discounting torsion angles. Under this definition,for example, proteins would be two dimensional, as would a plane ofgraphene. A covalent network solid or a carbon nanotube would bethree-dimensional.

A “tip” is a device for facilitating mechanosynthetic reactions whichincludes one or more “active” atoms or sites whose bonding pattern orelectronic state is altered during a mechanosynthetic operation, and oneor more “support” atoms whose bonding pattern or electronic state is notaltered during a mechanosynthetic operation. The support atoms functionto hold the active atoms in position.

“Tip swapping” is the process of connecting a new tip to a positionalmeans during a build sequence where said positional means already had aprevious tip to which it was connected.

A “tool” comprises a tip, potentially bonded to a handle, controlled bya positional device or means.

A “workpiece” is an apparatus, article of manufacture, or composition ofmatter, built via mechanosynthesis. A system may have more than oneworkpiece. A workpiece may be connected to, but does not include, otherstructures that were not created via mechanosynthesis, such as a supportsubstrates, feedstock depots, or tethered pre-existing structures.

Chemical Structure and Scientific Notation

A dot (“.”) is may be used in chemical structures herein to represent anelectron, as in the radical group “.CH2”. For ease of typesetting, thenotation herein generally omits subscript or non-standard characters.Superscript may be written using the “^” character when required forclarity.

Synthetic Tips

The instant invention addresses many problems related tomechanosynthesis, with at least some embodiments having one or more ofthe following benefits: avoiding the need for a bootstrap process,avoiding the need to build tips via mechanosynthesis, avoiding the needfor charging tips with feedstock during a build sequence, avoiding theneed to dispose of reaction byproducts, reducing the design complexityof new tips, and reducing or avoiding the need for multiple positionalmeans or tip switching. In addition, embodiments of the invention allowfor faster reaction throughput and longer tip travel distances whilestill maintaining sub-Angstrom accuracy.

Previous literature described (see, e.g., U.S. Pat. No. 9,244,097) abootstrap process to facilitate the creation of atomically-precise tipsfrom atomically-imprecise tips using mechanosynthesis. As an alternatemethod of directly preparing atomically-precise tips, we describe thebulk synthetic chemical preparation (and if appropriate, activation ordepassivation) of various atomically-precise tips, which can then bebonded to a presentation surface or tool. In this way,atomically-precise tips can be obtained without first usingatomically-imprecise tips.

Not only can synthetic tips be prepared in a different manner thanpreviously-known tips, but the manner in which synthetic tips are usedcan vary from the way previously-known tips are used in the literature.While synthetic tips could be used in the same manner aspreviously-described tips (e.g., via affixing a single synthetic tip toa handle), bulk preparation also allows other strategies to be employed.

For example, previous proposals describe rechargeable tips, usingstrategies that use a relatively small number of tips over and overagain during a build sequence. Because synthetic tips are available invery large numbers after synthesis, a large number of synthetic tipscould be affixed to a presentation surface. The synthetic tips can bepre-charged (meaning, the tips are already in the chemical state desiredto carry out the intended reactions, such as already being bonded tofeedstock), and they can include large numbers of every type of tiprequired for a given build sequence. In this way, the presentationsurface can serve purposes including being a feedstock depot (thesynthetic tips already being charged with their feedstock), a trashdepot (e.g., radical tips could be used to bind undesired atoms), and avaried collection of tips that can carry out all necessary reactions.Using a large number of synthetic tips allows each tip to be disposable,rather than requiring recharge for subsequent use, avoiding the need todesign and perform recharge operations. Note that in this scenario theworkpiece could be moved to the desired tip (“inverted mode”), ratherthan vice versa (“conventional mode”). Inverted mode is not necessary,but may be easier to implement on some equipment.

Conceptually, if the workpiece moves and the presentation surface isstationary, one could think of a build sequence as a workpiece movingaround a presentation surface, aligning itself with a desired tip, andthen being brought into contact with that tip with sufficient force totrigger the desired reaction. The tip that was used is then spent, butthe presentation surface can easily provide large numbers of tips (e.g.,depending on the size of the surface and the tip density, greater than athousand, or even a million, or a billion tips could be available). Thebuild sequence proceeds by then aligning the workpiece with the nextappropriate tip and bringing them together. This process repeats untilthe entre workpiece is built.

Other variations on this concept are also possible, including a toolwhich holds multiple tips (a “meta-tip”). Such designs may be moreefficient than a tool holding a single tip because multiple reactionscould be performed without requiring tips swapping or tip recharge.Whether the tips reside on a presentation surface, or on a tool, andwhether the presentation surface, the tool, the workpiece, or somecombination thereof are coupled to positional means, the overarchingpoint is a design which has at least some of the followingcharacteristics and advantages, among others.

First, a large number (e.g., more than a thousand even on a relativelysmall surface, while over a million or even over a billion is feasibleon a larger presentation surface) of tips may be available, whether on,for example, a conventional presentation surface (e.g., a silicon wafer)or a “meta-tip.” These tips may all be the same, or could be ofdifferent types. If multiple tip types are present, they could berandomly intermingled, segregated by sector or position, or the tipscould be laid out in an order which maximizes the efficiency of a buildsequence (for example, by arranging different tip sectors in a mannerthat minimizes the movement required to perform the mechanosyntheticoperations to build a particular workpiece, or considering a moregeneral design, locating tips that are apt to be used more frequentlycloser to the workpiece, or locating tip sectors concentrically around aworkpiece to minimize total tip to workpiece distance regardless of theorder of reactions).

Second, due to the large number of tips that are accessible to thesystem, tip recharge may be reduced or eliminated during a buildsequence. Each tip can be used once, and then ignored once it is spent.By eliminating recharge reactions, shorter, faster build sequences arefacilitated. If additional tips were still required, e.g., for aworkpiece requiring a number of tips beyond that which are available,the strategy of mounting a large number of tips, preferably in theirready-to-use state, on a surface, allows the bulk replacement of tips byswapping in a new surface. In this scenario, tip recharge is notcompletely eliminated, but it is greatly reduced.

Third, tips do not have to be swapped for chemical diversity becauseevery type of tip needed for a given build sequence can be presentsomewhere on the presentation surface. This reduces or eliminates theneed for multiple positional means, or the need to change the toolconnected to a single positional means.

Fourth, large numbers of atomically-precise tips can be prepared andaffixed via bulk chemical reactions (and similarly bulk activated, ifrequired). This eliminates the need for a bootstrap process that usesnon-atomically-precise tips to create atomically-precise tips. Exemplarysynthetic pathways for multiple synthetic tips are described herein.

Fifth, system complexity is kept relatively low, and the number of tipsand feedstock moieties available can be relatively high, as compared toother proposals for providing feedstock via, for example, methods whichrequire cartridges or conveyor belts (Rabani, “Practical method andmeans for mechanosynthesis and assembly of precise nanostructures andmaterials including diamond, programmable systems for performing same;devices and systems produced thereby, and applications thereof,” USPatent App 20090056802, United States, 2009).

Surface-Mounted Tips

Synthetic tips, if properly designed, can be chemically bound to apresentation surface, or “surface-mounted.” In addition to beingamenable to synthesis using traditional chemistry, and carrying out oneor more mechanosynthetic reactions, surface-mounted tips are designed toallow efficient bonding to a presentation surface or handle structure(often in large quantity).

Surface-mounted tips differ from conventional tips in that they are notsimply integral to a handle structure (e.g., commercially available tipsoften have a tip where the crystal structure of the tip is contiguouswith the handle structure; essentially the tip is just the end of thehandle structure), nor are they a handle structure to which only atrivial functionalization has been added (e.g., bonding a single CO tothe end of an existing tip is a common technique to increaseresolution). Surface-mounted tips differ from previously-proposedmechanosynthetically-created tips in that they do not requiremechanosynthesis to manufacture (which has not only processimplications, but structural and chemical implications since thisrequires that surface-mounted tips be able to bind to the desiredsurface without the aid of mechanosynthesis). Given this, whilesurface-mounted tips may look similar to other tips described in theliterature, the requirements for the design of tips which are to besurface-mounted are substantially different.

Binding orientation is one issue that must be addressed when designingsurface-mounted tips. It would be preferable that the tips only be ableto affix themselves to a surface in a manner that renders them properlyoriented for use in mechanosynthetic reactions (although multiplepossible orientations could be acceptable given the number of redundanttips that could be present—the system could then scan to identify anduse only tips in the desired orientation, but this reduces efficiency).

Active sites and legs are discussed in more detail herein, but are majorfactors in ensuring that correct binding orientation is obtained. Forexample, tips with radical active sites will be highly reactive in theiractive form. Due to this high reactivity, the active site may bind tothe presentation surface instead of the legs. If this happens, the tipwould end up bound to the presentation surface upside down. Reactivesites may also form bonds to other parts of the same tip, or may formbonds to other tips, such as two tips dimerizing. This problem may beavoided in the case of reactive active sites by binding the tip to thepresentation surface with the active sites neutralized. The active sitescan then be activated after leg binding. A similar issue presents itselfwith respect to the legs. The legs (or leg linkers) need to be reactiveenough that they will bind to the presentation surface, but they mustresist pathological reactions with themselves or other tips (e.g.,forming a leg-leg bond instead of a leg-surface bond, or undergoing anyother undesired reactions).

Of course, there are other design consideration for tips, including thatthey perform the desired reactions reliably during a build sequence, butthe above concerns are unique to bulk-synthesized, surface-mounted tips.Tips created using mechanosynthesis can largely avoid these problems viapositional specificity. Further, mechanosynthetically-created tips havedifferent design constraints due to the different methods ofconstruction (e.g., as will be explained later, one way to attachsynthetic tips to a surface involves chlorinating the surface, whichintroduces its own design constraints; chlorination could be avoided orremoved as needed using mechanosynthesis). Although for differentreasons, conventional tips avoid such problems (and therefore designconstraints) as well. For example, tips which are simply ultra-sharpcontinuations of a handle structure need not worry about orientation orother pathological binding considerations.

Modular Tip Design

As will be seen in subsequent examples, surface-mounted tips can bethought of as being modular. Each tip can be thought of as having anactive site (one or more atoms that bind a desired atom or group ofatoms, which could be, e.g., feedstock for a donation reaction, or somemoiety to be removed from a workpiece for an abstraction reaction), abody (adamantane or an adamantane derivative in our examples, but otherstructures obviously could be used), and one or more legs that serve toattach the tip to a surface. The feedstock of a tip could also beconsidered a module, as could the surface, which, although nottechnically part of the tip, can be important to tip design andfunction.

To aid in understanding how tips function, and how they can berationally designed, considerations pertinent to each module aredescribed below. Note that the specific examples presented useadamantane, or adamantane-like bodies. Many reactions forfunctionalizing adamantanes are known, and their stiffness, small size,computational tractability and other favorable characteristics lead usto use these structures as exemplary tips, although obviously manydifferent molecules, including other adamantane-like structures, couldserve the same purpose.

The active site's main characteristic is that it reliably facilitate thedesired reaction on a workpiece. However, how to efficiently synthesizeand deliver tips to a surface, and prepare them for use, must beconsidered in their design. Particularly when containing a radical inits ready-to-use state, a tip may incorporate a protective cap (what insolution-phase chemistry is commonly referred to as a “protectinggroup”). This cap reduces the active site's reactivity prior to use toavoid, for example, tip-tip dimerization, binding of the active site tothe surface, or other undesired reactions. However, the cap must beremovable so that the tip can be activated for use. One way to do thisis to make the cap photo-cleavable, but obviously other methods arepossible as long as they selectively remove the desired caps withoutharming any tips that may be present.

The body serves as a point of attachment for the active site and legs,and can also serve to tune the active site, and to isolate it from otherchemical influences. With respect to tuning the active site, forexample, substitutions which alter bond lengths, angles, orelectronegativity may be used to increase or decrease the affinity ofthe active site for its feedstock or whatever moiety it is intended tobind. With respect to isolation, the body provides chemical isolationfrom, for example, the legs. Such isolation is one of the aspects ofthis modular design paradigm that eases the design of new tips byallowing modules to be put together combinatorially. For example, if anactive site and body combination that accomplish the desired reactionare already known, but one desires to use a different surface whichnecessitates different legs or linkers, it is likely that the new partscan be swapped in without redesign of the body and active site. If thelegs were connected directly to the active site, their chemical naturewould tend to have more of an effect on the active site, potentiallyrequiring more redesign. Another characteristic of the body is that itis preferably rigid. A rigid body, while not required, will tend to bemore versatile because a rigid body will better resist deformation whenpressed on during reaction with a barrier that must be overcome.

The legs serve to attach the body to the surface. The legs preferablyhave a geometry that permits them to bind the body to a surface withoutexcessive strain, including surfaces that are functionalized prior toleg attachment. Functionalized surfaces, such as chlorinated Si, maymake longer legs preferable because the, e.g., Cl atoms, can be directlyunder the tip body, make some clearance between the body of the tip andSi itself preferable. Legs are also preferably fairly rigid, and strongenough so that reactions require the application of force to overcome abarrier proceed reliably rather than the tip tilting, otherwise moving,or breaking a leg bond. While legs that are too short may be unable tobond to the surface reliably, legs that are too long may be tooflexible, adding to the positional uncertainty of the tip atoms during amechanosynthetic operation. Where issues such as surfacefunctionalization and lattice mismatches are not issues, legs can bevery short (e.g., a single oxygen atom could serve as each leg).

With respect to the number of legs, the examples provided depict tipswith three legs. This helps provide stability for reactions whichrequire the application of force to the tip. Tips with less than threelegs, or more than three legs, or tips where not all of the linkers havebound to the surface, could also be used as long as the requiredstability is provided. On a tip with multiple legs, each leg does notneed to be identical.

Legs may incorporate linkers (if not, the leg may be considered to alsobe the linker, or vice versa), which serve to provide a bridge betweenthe rest of the leg and the body or surface. The advantage of linkers isin providing an appropriate chemistry with which to bind a surface. Forexample, if the rest of the leg does not have the necessary reactivityor bond strength with a surface, a linker may address the issue, asdemonstrated with the exemplary O, NH, and S linkers in the examplesherein. Linkers may also be used to adjust the geometry of the legs, forexample, helping them to fit the surface lattice spacing better, oradjusting their length or rigidity.

Feedstock serves as a source of atoms which can be added to a workpiece.Feedstock is chosen not only by what atom or atoms is contains, but byhow it binds to a tip's active site and the desired location on aworkpiece. There are many ways, for example, to donate carbon atoms to aworkpiece, and examples using C2, CH2, and CH3 are all presented herein.Context will determine which is most appropriate, though often more thanone could be used to build a given workpiece, assuming appropriatealterations in the build sequence.

The surface to which a tip is being attached has a variety of importantcharacteristics, including chemical reactivity, surface smoothness,lattice spacing, linker-surface bond strength, and internal bondstrength. In terms of chemical reactivity, the surface must bind to thelinkers, but preferably no other parts of the tip. The surface's latticespacing must allow linker binding without excessive strain. Thelinker-surface bond strength must suffice so that the bonds do notrupture if pulling forces are required. And, the internal(surface-surface) bonds must be of sufficient strength that, if pullingforces are required, the entire tip, along with one or more surfaceatoms, is not ripped from the surface.

With surface-mounted tips being broken down into the described modules,and the important functional characteristics of each module described,and realizing that this modular design at least to an extent isolatesvarious modules from one another, facilitating module re-use andcombinatorial creational of new tips, along with the examples presentedherein, this provides a design paradigm for the design and synthesis ofnew tips that can be generalized well beyond the specific examplesprovided.

FIG. 1 depicts one version of an abstraction tip that may be used toremove hydrogen, among other moieties, from a workpiece. Radical 101 isused to bind the moiety to be abstracted, and serves as the tip's activesite. The active site is connected to body 102, which in this example isadamantane. The body is connected to three methyl group legs,exemplified by leg 103. Each leg is connected to a sulfur linker,exemplified by linker 104. Each linker is bound to surface 105. As anabstraction tip, no feedstock is present.

As a different example, with feedstock, FIG. 2 depicts one version of atip capable of donating hydrogen to many atom types. Active site 201 isa Ge atom, which in this case is part of a substituted adamantane body202. Trifluorobenzene (which could be viewed as trifluorophenol if thelinkers were considered to be part of this structure) legs are used,exemplified by leg 203, and each leg is connected to an oxygen linker204, which connects to surface 205. Feedstock 206 is connected to activesite 201.

Exemplary Tips

Surface-mounted tips, along with their routes of synthesis, have beendevised which carry out mechanosynthetic reactions while minimizing oreliminating issues such as tip dimerization and improper tip orientationduring surface mounting, and allow for proper leg length and flexibilityand proper linker chemistry to bind to the exemplary surfaces. Thesesynthetic routes allow for the bulk manufacture of many diverse tiptypes, thereby facilitating many different mechanosynthetic reactionswhile having the benefits described for surface-mounted tips and theprocesses for using such tips.

The set of tips described includes an abstraction tip with a C2-basedactive site (capable of extracting many atoms from many different typesof workpieces, including, e.g., hydrogen from diamond), a hydrogendonation tip, a C2 donation tip, a Methyl donation tip, and a donationtip which can donate SiH3, GeH3, Si(CH3)3, or Ge(CH3)3, depending on thefeedstock attached to the Ge active atom in its substituted adamantanebody.

To demonstrate the modular design described herein, various versions ofeach tip are depicted. Specially, each tip is shown with threetrifluorobenzene legs which can be linked to either a chlorinatedsilicon surface, or partially-hydrogenated partially-chlorinated siliconsurface, via an oxygen linker or an NH linker. A version of each tip isalso depicted where the legs are methyl groups, using sulfur linkers toconnect to an Au surface. These various versions provide for a varietyof surface properties and surface attachment chemistries and demonstratehow a body can be used to isolate an active site from other changes inthe tip, as the tips continue to function as desired after changing thelegs, linkers, and surface.

Note that a silicon surface has stronger intra-surface bonds than a goldsurface. When placing tips on a gold surface, reactions that requiresubstantial pulling forces (exceeding a few nN) may pull the tip fromthe surface (taking one or more gold atoms with it), or cause the tip toslide sideways across the surface. Nonetheless, the thiol linkerchemistry is very accessible, making gold a useful surface (along withlead and other similar materials) if reactions with substantial pullingforces are not required.

Each exemplary tip is shown in detail, bonded to an appropriate surfacefor the linker chemistry depicted, in FIGS. 3-17. FIGS. 3-7 all depicttips that use trifluorobenezene legs and oxygen linkers on a siliconsurface. Specifically: FIG. 3 depicts an abstraction tip having aC2-radical-based active site, an adamantane body, trifluorobenzene legs,and oxygen linkers, on a silicon surface (all Si surfaces include, e.g.,chlorinated, partially-chlorinated, and partially-hydrogenated,partially-chlorinated Si). This tip will be referred to as AbstractO.FIG. 4 depicts a hydrogen donation tip with hydrogen feedstock, aGe-based active site incorporated into a substituted adamantane body,trifluorobenzene legs, and oxygen linkers, on a silicon surface. Thistip will be referred to as HDonationO. FIG. 5 depicts a C2 donation tipwith .C2 feedstock, and otherwise the same structure as FIG. 4. This tipwill be referred to as C2DonationO. FIG. 6 depicts a methyl donation tipwith .CH2 feedstock, and otherwise the same structure as FIG. 4. Thistip will be referred to as MeDonationO. FIG. 7 depicts a donation tipthat can be used to donate a variety of feedstock moieties depending onthe identity of the M and R groups. M can be Si or Ge, and R can be H orCH3, allowing the tip to donate SiH3, GeH3, Si(CH3)3 or Ge(CH3)3. Thesetips will be referred to, respectively, as SiH3DonationO, GeH3DonationO,SiMe3DonationO, and GeMe3DonationO. FIG. 7 has otherwise the samestructure as FIG. 4

FIGS. 8-12 depict tips with the same feedstock (if present), activesite, bodies, and legs as FIGS. 3-7, respectively, but each tip in FIGS.8-12 uses NH linkers instead of oxygen linkers to connect to a siliconsurface. These tips will be referred to, respectively, as AbstractionNH,HDonationNH, C2DonationNH, MeDonationNH, and for the various versions ofFIG. 12, SiH3DonationNH, GeH3DonationNH, SiMe3DonationNH, andGeMe3DonationNH.

FIGS. 13-17 depict tips with the same feedstock (if present), activesite, and bodies as FIGS. 3-7, respectively, but each tip in FIGS. 13-17uses methyl legs and a sulfur atom linker to connect the tip to a goldsurface. These tips will be referred to, respectively, as AbstractionS,HDonationS, C2DonationS, MeDonationS, and for the various versions ofFIG. 17, SiH3DonationS, GeH3DonationS, SiMe3DonationS, andGeMe3DonationS.

In addition to the use of these tips in their charged state, some tipscould be used in their uncharged state. For example, several of thetips, such as the hydrogen donation tip, have a Ge radical active sitein their discharged state. This can actually be a useful tip itself, forexample, to break into a C═C bond.

Tip Synthesis

Exemplary synthetic pathways for each tip are depicted in FIGS. 18-41.Note that multiple synthetic pathways for the tip depicted in FIGS. 7,12 and 17 due to the various possible combinations of M and R. Tips withradicals in their active form are synthesized with a protective cap.Procedures for cap removal are described herein.

FIG. 18 depicts a synthetic pathway for AbstractO. The synthesis stepsare as follows: Commercially available 1,3,5-trihydroxyadamantane reactswith 2,4,6-trifluorophenol while heated between 50-80° C. under acidicconditions to give OFA-1. Treating OFA-1 with an excessdimethyldioxirane (DMDO) in acetone at room temperature selectivelyoxidizes the tertiary C—H bond to give alcohol OFA-2. Using Koch-Haafconditions (Stetter, H., Schwarz, M., Hirschhorn, A. Chem. Ber. 1959,92, 1629-1635), CO is formed from the dehydration of formic acid byconcentrated sulfuric acid between −5-0° C. The CO forms a bond with thetertiary carbocation formed from the dehydration of the bridgeheadalcohol at room temperature. Upon aqueous workup the carboxylic acidOFA-3 is obtained. Esterification of the carboxylic acid OFA-3 with drymethanol and catalytic sulfuric acid between 40-60° C. yields the methylester OFA-4. The phenolic —OH groups in OFA-4 are protected withtert-butyldimethylsilyl chloride (TBSCl) in the presence of imidazole atroom temperature to give the TBS-silyl ether OFA-5. Reduction of themethyl ester with LiAlH4 in tetrahydrofuran (THF) between 0° C. and roomtemperature gives the methyl alcohol OFA-6. Oxidation of the methylalcohol to the aldehyde OFA-7 proceeds with catalytictetrapropylammonium perruthenate ((Pr4N)RuO4, TPAP) and stoichiometricN-methylmorpholine-N-oxide (NMO). The presence of 4 Å powdered molecularsieves in the reaction mixture adsorbs any water present and decreasesthe probability of over-oxidation to the carboxylic acid (Ley, S. V.,Norman, J., Griffith, W. P., Marsden, S. P., Synthesis, 1994, 639-666).Using a modified Corey-Fuchs procedure (Michel, P., Rassat, A.Tetrahedron Lett. 1999, 40, 8570-8581), the aldehyde in THF is added toa premixed solution of iodoform (CHI3), triphenylphosphine, andpotassium tert-butoxide at room temperature in THF to undergo acarbon-carbon bond forming reaction to give the 1,1-diiodoalkene. Singleelimination of the vinyl iodide with excess potassium tert-butoxide andcareful temperature control (−78° C.-−50° C.) yields the iodoalkyneOFA-8. It is possible to form the terminal alkyne from this reaction iftemperature is not carefully controlled, however, the terminal alkynecan be iodinated with N-iodosuccinimide/AgNO3 or, alternatively, with I2in basic methanol. The final global deprotection of the TBS-silyl ethergroups is performed with tetra-n-butylammonium fluoride (TBAF). Uponaqueous workup, the AbstractO tip with free phenol linkers OFA-9 isobtained.

FIG. 19 depicts a synthetic pathway for HDonationO. The synthesis stepsare as follows: FHD-104X is reduced by excess lithium aluminum hydridein THF solvent at 0° C., converting the germanium halide to thegermanium hydride FHD-105. Tetra-n-butylammonium fluoride is used todeprotect the tert-butyldimethylsilyl protecting groups from FHD-105 inTHF to yield the triphenol FHD-106, the HdonationOHtip.

FIG. 20 depicts a synthetic pathway for C2DonationO. The synthesis stepsare as follows: The Grignard reagent ethynylmagnesium bromide in THFsolution is added to FHD-104X dissolved in dry THF and cooled to −78 Cdropwise with rapid stirring. The reaction is stirred for 1 hour, warmedto 0 C for 1 hour, and stirred for 1 hour at room temperature to formFC2D-101. FC2D-101 is dissolved in dry THF and cooled to −78 C. Asolution of n-butyllithium in hexanes is added and the reaction isstirred for 1 hour at −78 C. A solution of iodine in dry THF is addedand the reaction is allowed to warm to room temperature to yieldFC2D-102. FC2D-102 is dissolved in THF and stirred rapidly at roomtemperature. Tetra-n-butylammonium fluoride is added and the reaction isstirred for 1 hour to yield FC2D-103, the C2DonationO tip.

FIG. 21 depicts a synthetic pathway for MeDonationO. The synthesis stepsare as follows: The germanium halide FHD-104X in THF solution is reducedwith lithium metal to generate a lithiated germanium species in situ.The solution is then slowly added dropwise to a solution of 10-foldexcess methylene iodide (CH2I2) in THF cooled to 0 C. This method ofaddition favors the formation iodomethyl germane FMeD-101 overmethylene-bridged germanes. Stoichiometric tetra-n-butylammoniumfluoride is used to deprotect the tert-butyldimethylsilyl protectinggroups from FMeD-101 in THF to yield the triphenol FMeD-102, theMeDonationO tip.

FIG. 22 depicts a synthetic pathway for SiH3DonationO. The synthesissteps are as follows: The phenols of FHD-106 are acylated with mesitoylchloride in dichloromethane with pyridine base. (Corey et al., JACS1969, 91, 4398) The mesitoate protecting group is utilized due to itsstability to the lithiation conditions necessary for FSiHD-102.FSiHD-101 in dry THF solution is deprotonated with n-butyllithium inhexanes at −78 C and slowly warmed to room temperature. The resultinglithiated anion is silylated with chlorotriethoxysilane in THF solutionto yield FSiHD-102. FSiHD-102 in dry THF solution is cooled to 0 C andlithium aluminum hydride in THF solution is added to cleave themesitoate esters and reduce the triethoxysilyl group, yieldingFSiHD-103, the SiH3DonationO tip.

FIG. 23 depicts a synthetic pathway for GeH3DonationO. The synthesissteps are as follows: To form FGeHD-101, the germanium halide FHD-104Xin THF solution is reduced with lithium metal to generate a lithiatedgermanium species in situ. The solution is then removed by syringe toseparate the lithiated germanium species from the unreacted lithiummetal and then slowly added dropwise to a solution ofchloro(phenyl)germane (Ohshita, J.; Toyoshima, Y.; Iwata, A.; Tang, H.;Kunai, A. Chem. Lett. 2001, 886-887) in THF cooled to 0 C. It isnecessary to separate the lithiated germanium species from excesslithium metal before addition to the trimethylgermanium chloride becauselithium is capable of exchange reactions with germanium halides.FGeHD-101 is dephenylated with trifluoromethanesufonic acid indichloromethane at 0 C. The crude reaction isolate after neutralizationand workup is then dissolved in dry THF. The reaction is cooled to 0 Cand lithium aluminum hydride is added dropwise to produce the germaneFGeHD-102, the GeH3DonationO tip.

FIG. 24 depicts a synthetic pathway for SiMe3DonationO. The synthesissteps are as follows: To prepare FSiHD-101, the phenols of FHD-106 areacylated with mesitoyl chloride in dichloromethane with pyridine base.(Corey et al., JACS 1969, 91, 4398) The mesitoate protecting group isutilized due to its stability to the lithiation conditions necessary forFSiHD-102. FSiHD-101 in dry THF solution is deprotonated withn-butyllithium in hexanes at −78 C and slowly warmed to roomtemperature. The resulting lithiated anion is silylated withtrimethylsilyl chloride in THF solution to yield FSiMeD-102. FSiMeD-102in dry THF solution is cooled to 0 C and lithium aluminum hydride in THFsolution is added to cleave the mesitoate esters, yielding FSiMeD-103,the SiMe3DonationO tip.

FIG. 25 depicts a synthetic pathway for GeMe3DonationO. The synthesissteps are as follows: To prepare FGeMeD-101, the germanium halideFHD-104X in THF solution is reduced with lithium metal to generate alithiated germanium species in situ. The solution is then removed bysyringe to separate the lithiated germanium species from the unreactedlithium metal and then slowly added dropwise to a solution oftrimethylgermanium chloride in THF cooled to 0 C. It is necessary toseparate the lithiated germanium species from excess lithium metalbefore addition to the trimethylgermanium chloride because lithium iscapable of exchange reactions with germanium halides. Stoichiometrictetra-n-butylammonium fluoride is used to deprotect thetert-butyldimethylsilyl protecting groups from FMeD-101 in THF to yieldthe triphenol FGeMeD-102, the GeMe3DonationO tip.

FIG. 26 depicts a synthetic pathway for AbstractNH. The synthesis stepsare as follows: Commercially available 1,3,5-trihydroxyadamantane reactswith 2,4,6-trifluoroaniline while heated to 50-80° C. under acidicconditions in 1,2-dichloroethane to give NFA-1. Treating NFA-1tetrafluoroboric acid forms the tetrafluoroborate amine salt in situ toprevent oxidation of the amines. (Asencio, G., Gonzalez-Nuñez, M. E.,Bernardini, C. B., Mello, R., Adam, W. J. Am. Chem. Soc., 1993, 115,7250-7253) Following the salt formation, an excess of dimethyldioxirane(DMDO) in acetone at room temperature selectively oxidizes the tertiaryC—H bond to give alcohol NFA-2. Using Koch-Haaf conditions (Stetter, H.,Schwarz, M., Hirschhorn, A. Chem. Ber. 1959, 92, 1629-1635), CO isformed from the dehydration of formic acid by concentrated sulfuricacid. The CO forms a bond with the tertiary carbocation formed from thedehydration of the bridgehead alcohol. Upon aqueous workup thecarboxylic acid NFA-3 is obtained. Esterification of NFA-3 with drymethanol and catalytic sulfuric acid yields the ester NFA-4 that can bereduced readily with diisobutylaluminum hydride.Di-tert-butyl-dicarbonate (Boc2O) is used to protect the —NH2 groups andto be removable by acid hydrolysis. Treating NFA-4 with Boc2O yields theprotected compound NFA-5. Reduction of the methyl ester with LiAlH4 intetrahydrofuran (THF) gives the methyl alcohol NFA-6. Oxidation of themethyl alcohol to the aldehyde NFA-7 proceeds with catalytictetrapropylammonium perruthenate (TPAP) and stoichiometricN-methylmorpholine-N-oxide (NMO). The presence of 4 Å powdered molecularsieves in the reaction mixture adsorbs any water present and decreasesthe probability of over-oxidation to the carboxylic acid. (Ley, S. V.,Norman, J., Griffith, W. P., Marsden, S. P., Synthesis, 1994, 639-666)Using a modified Corey-Fuchs procedure (Michel, P., Rassat, A.Tetrahedron Lett. 1999, 40, 8570-8581), the aldehyde in THF is added toa premixed solution of iodoform (CHI3), triphenylphosphine, andpotassium tert-butoxide at room temperature in THF to undergo acarbon-carbon bond forming reaction to give the 1,1-diiodoalkene. Singleelimination of iodide with careful temperature (−78° to −50° C.) andexcess potassium tert-butoxide control yields the iodoalkyne NFA-8. Itis possible to form the terminal alkyne from this reaction iftemperature is not carefully controlled, however, the terminal alkynecan be iodinated with N-iodosuccinimide/AgNO3 or, alternatively, with I2in basic methanol. The final global deprotection of the Boc-groups isperformed with trifluoroacetic acid (TFA) in dichloromethane at RT. Uponaqueous workup, NFA-9, the AbstractNH tip, is obtained.

FIG. 27 depicts a synthetic pathway for HDonationNH. The synthesis stepsare as follows: NHD-103X in dry THF solution is cooled to 0 C andlithium aluminum hydride in THF solution is added to reduce thegermanium halide, yielding NHD-104. NHD-104 is dissolved in dry MeOH andadded to a reaction vessel suitable for pressurized hydrogenations.Palladium hydroxide catalyst is added and the vessel pressurized withhydrogen gas. Agitation of the reaction under the pressurized hydrogenatmosphere yields NHD-105, the HDonationNH tip.

FIG. 28 depicts a synthetic pathway for C2DonationNH. The synthesissteps are as follows: (Triisopropylsilyl)acetylene is dissolved in dryTHF and cooled to −78 C. n-Butyllithium solution in hexanes is slowlyadded dropwise to deprotonate the acetylene hydrogen. The solution isstirred for 1 hour, allowed to warm to room temperature, and is addeddropwise to NHD-103X in dry THF solution cooled to −78 C. The reactionis stirred for 1 hour, warmed to 0 C for 1 hour, and stirred for 1 hourat room temperature to form NC2D-101. NC2D-101 is dissolved in dry MeOHand added to a reaction vessel suitable for pressurized hydrogenations.Palladium hydroxide catalyst is added and the vessel pressurized withhydrogen gas. Agitation of the reaction under the pressurized hydrogenatmosphere yields NC2D-102. The steric bulk of both thetriisopropylsilyl group and the germaadamantane core preventhydrogenation of the alkyne. NC2D-102 is dissolved in THF and stirredrapidly at room temperature. Tetra-n-butylammonium fluoride is added andthe reaction is stirred for 1 hour at RT to yield NC2D-103. NC2D-103 isdissolved in MeOH and rapidly stirred. Potassium hydroxide is added anda solution of iodine in methanol is added slowly dropwise at RT to yieldNC2D-104, the C2DonationNH tip.

FIG. 29 depicts a synthetic pathway for MeDonationNH. The synthesissteps are as follows: The germanium halide NHD-103X in THF solution isreduced with lithium metal to generate a lithiated germanium species insitu. The solution is then slowly added dropwise to a solution of10-fold excess methylene iodine (CH2I2) in THF cooled to 0 C. Thismethod of addition favors the formation iodomethyl germane NMeD-101 overmethylene-bridged germanes. NMeD-101 is dissolved in dry MeOH and addedto a reaction vessel suitable for pressurized hydrogenations. Palladiumhydroxide catalyst is added and the vessel pressurized with hydrogengas. Agitation of the reaction under the pressurized hydrogen atmosphereyields NMeD-102, the MeDonationNH tip.

FIG. 30 depicts a synthetic pathway for SiH3DonationNH. The synthesissteps are as follows: The germanium halide NHD-103X in THF solution isreduced with lithium metal at −78 C to generate a lithiated germaniumspecies in situ. The solution is then removed by syringe to separate thelithiated germanium species from the unreacted lithium metal and thenslowly added dropwise to a solution of excess chlorotriethoxysilane inTHF cooled to 0 C and the reaction is allowed to warm to roomtemperature to produce NSiHD-101. NSiHD-101 in THF solution cooled to 0C is reduced with lithium aluminum hydride to generate NSiHD-102.NSiHD-102 is dissolved in cyclohexane and added to a reaction vesselsuitable for pressurized hydrogenations. Palladium hydroxide catalyst isadded and the vessel pressurized with hydrogen gas. Agitation of thereaction under the pressurized hydrogen atmosphere yields NSiHD-103, theSiH3DonationNH tip.

FIG. 31 depicts a synthetic pathway for GeH3DonationNH. The synthesissteps are as follows: The germanium halide NHD-103X in THF solution isreduced with lithium metal at −78 C to generate a lithiated germaniumspecies in situ. The solution is then removed by syringe to separate thelithiated germanium species from the unreacted lithium metal and thenslowly added dropwise to a solution of chloro(phenyl)germane in THFcooled to 0 C and the reaction is allowed to warm to room temperature toproduce NGeHD-101. It is necessary to separate the lithiated germaniumspecies from excess lithium metal before addition to thetrimethylgermanium chloride to prevent lithium-halogen exchangereactivity with the chloro(phenyl)germane. NGeHD-101 is dephenylatedwith trifluoromethanesufonic acid at 0 C. The crude reaction isolateafter neutralization of acid and workup is then dissolved in dry THF.The reaction is cooled to 0 C and lithium aluminum hydride is added toproduce the germane NGeHD-102. NGeHD-102 is dissolved in cyclohexane andadded to a reaction vessel suitable for pressurized hydrogenations.Palladium hydroxide catalyst is added and the vessel pressurized withhydrogen gas. Agitation of the reaction under the pressurized hydrogenatmosphere yields NGeHD-103, the GeH3DonationNH tip.

FIG. 32 depicts a synthetic pathway for SiMe3DonationNH. The synthesissteps are as follows: The germanium halide NHD-103X in THF solution isreduced with lithium metal at −78 C to generate a lithiated germaniumspecies in situ. The solution is then removed by syringe to separate thelithiated germanium species from the unreacted lithium metal and thenslowly added dropwise to a solution of excess chlorotrimethylsilane inTHF cooled to 0 C and the reaction is allowed to warm to roomtemperature to produce NSiMeD-101. NSiMeD-101 is dissolved incyclohexane and added to a reaction vessel suitable for pressurizedhydrogenations. Palladium hydroxide catalyst is added and the vesselpressurized with hydrogen gas. Agitation of the reaction under thepressurized hydrogen atmosphere yields NSiMeD-102, the SiMe3DonationNHtip.

FIG. 33 depicts a synthetic pathway for GeMe3DonationNH. The synthesissteps are as follows: The germanium halide NHD-103X in THF solution isreduced with lithium metal at −78 C to generate a lithiated germaniumspecies in situ. The solution is then removed by syringe to separate thelithiated germanium species from the unreacted lithium metal and thenslowly added dropwise to a solution of trimethylgermanium chloride inTHF cooled to 0 C and the reaction is allowed to warm to roomtemperature to produce NGeMeD-101. It is necessary to separate thelithiated germanium species from excess lithium metal before addition tothe trimethylgermanium chloride to prevent lithium reduction of thegermanium chloride. NGeMeD-101 is dissolved in cyclohexane and added toa reaction vessel suitable for pressurized hydrogenations. Palladiumhydroxide catalyst is added and the vessel pressurized with hydrogengas. Agitation of the reaction under the pressurized hydrogen atmosphereyields NGeMeD-102, the GeMe3DonationNH tip.

FIG. 34 depicts a synthetic pathway for AbstractS. The synthesis stepsare as follows: Commercially available 1-bromoadamantane undergoes aFriedel-Crafts alkylation with three separate benzene molecules underLewis acidic conditions with AlCl3 at 90 C to yield SHA-1. Carefulcontrol of the stoichiometry of the tert-butyl bromide (2.0 equivalents)yields the 1,3,5-triphenyl adamantane (Newman, H. Synthesis, 1972, 12,692-693). Treatment of SHA-1 in fluorobenzene and 50% aqueous NaOHsolution with a phase transfer catalyst gives SHA-2. This reaction isselective at brominating the tertiary C—H bond in the adamantane(Schreiner, P. R.; Lauenstein, O.; Butova, E. D.; Gunchenko, P. A.;Kolomitsin, I. V.; Wittkopp, A.; Feder, G.; Fokin, A. A., Chem. Eur. J.2001, 7, 4996-5003). Oxidative cleavage of the aromatic rings by RuCl3in a biphasic mixture gives the tricarboxylic acid SHA-3 (Carlsen, P. H.J.; Katsuki, T.; Martin, V. S.; Sharpless, K. B., J. Org. Chem. 1981,46, 3936-3938). Esterification of SHA-3 with dry methanol and catalyticsulfuric acid between 50-60° C. yields the triester SHA-4 that can bereduced readily with LiAlH4 at 0 C. The triol SHA-4 can react readilywith triflic anhydride and pyridine in dichloromethane at 0 C to givethe compound SHA-5. Condensing vinyl bromide at −20° C. with catalyticAlBr3 in the presence of the adamantyl bromide SHA-5 gives adibromoethyladamantane intermediate that is used with potassiumtert-butoxide to eliminate to give the alkyne SHA-6 (Malik, A. A.;Archibald, T. G.; Baum, K.; Unroe, M. R., J. Polymer Sci. Part A:Polymer Chem. 1992, 30, 1747-1754). Three equivalents of potassiumthioacetate displaces the triflate groups in refluxing acetonitrile togive the compound SHA-7. The use of 18-crown-6 enhances thenucleophilicity of the thioacetate and can be added to enhance the rateof the reaction at room temperature (Kitagawa, T., Idomoto, Y.;Matsubara, H.; Hobara, D.; Kakiuchi, T.; Okazaki, T.; Komatsu, K., J.Org. Chem. 2006, 71, 1362-1369). Silver nitrate with N-iodosuccinimidein THF creates the iodoalkyne at room temperature and treatment withpotassium hydroxide removes the acetate groups to give compound SHA-8,the AbstractS tip.

FIG. 35 depicts a synthetic pathway for HDonationS. The synthesis stepsare as follows: Allowing RHD-101 to react with benzene andtrifluoroacetic acid (TFA) at room temperature in dichloromethane formsthe triphenylgermaadamantane SHD-101. Oxidative cleavage of the phenylgroups with catalytic RuCl3 in a solvent mixture of CCl4, CH3CN, and H2Owith periodic acid added as stoichiometric oxidant cleaves the aromaticrings between 0° C. to room temperature gives the tricarboxylic acidSHD-102. Esterification of SHD-102 with methanol with sulfuric acidbetween 40-60° C. gives the triester that can subsequently be reducedwith LiAlH4 at 0° C. to give the triol SHD-103. Triol SHD-103 can betreated with triflic anhydride at 0° C. with pyridine in dichloromethaneto give the triflate SHD-104. Displacement of the triflate groups withpotassium thioacetate in the presence of 18-crown-6 ether inacetonitrile at room temperature yields the acetate-protected thiols inSHD-105. Treatment of SHD-105 with a Lewis acid source including to butnot limited to SnCl4, I2, or Br2 in dichloromethane at −78° C. to roomtemperature selectively cleaves the Ge-Me bond to give the respectiveGe—X (X=Cl, Br, I) bond in SHD-106X. Treating the resulting Ge—Xcompound SHD-106X with LiAlH4 at 0° C. to room temperature reduces theGe—X bond as well as simultaneously removing the thioacetate groups fromthe thiols to yield the trithiol SHD-107, the HDonationS tip, uponaqueous workup.

FIG. 36 depicts a synthetic pathway for C2DonationS. The synthesis stepsare as follows: The intermediate SHD-106X from the HDonationS synthesisis allowed to react with an excess of commercially availableethynylmagnesium bromide solution in diethyl ether at 0° C. to roomtemperature to form SC2D-101. The excess of the ethynylmagnesium bromideensures full deprotection of the thioacetate protective groups uponaqueous workup. The thiols in SC2D-101 are protected with acetate groupsby treating it with acetic anhydride (Ac2O). The protected compound isthen treated with silver nitrate and a slight excess ofN-iodosuccinimide in THF at room temperature to form the iodoalkyne inSC2D-102. Subsequent treatment of the crude reaction mixture in basicmethanol at room temperature yields SC2D-102, the C2DonationS tip.

FIG. 37 depicts a synthetic pathway for MeDonationS. The synthesis stepsare as follows: The synthesis of the thiol methyl donation tool beginsfrom intermediate SHD-105. The acetate groups must be exchanged with athioether protective group, specifically the tert-butyl group, towithstand the synthetic conditions. The acetate groups are removed inbasic methanol at room temperature and then subsequently treated with anacidic solution of tert-butanol at room temperature to form SMeD-101.The Ge—Me bond is cleaved with a Lewis acid between −78° C. and roomtemperature with a reagent such as SnCl4, 12, or Br2 to yield the Ge—Clbond in SMeD-102X. Treating SMeD-102X with lithium metal and excessCH2I2 at 0 C in THF at high dilution yields SMeD-103. Removal of thetert-butyl groups is performed with 2-nitrobenzenesulfenyl chloride inacetic acid and yields a mixed disulfide (Pastuszak, J. J., Chimiak, A.,J. Org. Chem., 1981, 46, 1868. Quintela, J. M., Peinador, C.,Tetrahedron, 1996, 52, 10497). Treating this disulfide with NaBH4 at lowtemperature between −20° C. and 0° C. allows the recovery of the freethiol SMeDon-104, the MeDonationS tip, without reducing the C—I bond.

FIG. 38 depicts a synthetic pathway for SiH3DonationS. The synthesissteps are as follows: Intermediate SMeD-102X with t-butyl protectedthiols is treated with lithium metal in THF at 0° C. followed by theaddition of triethoxychlorosilane to give SSiHD-101 upon workup. Thisreaction forms the Ge—Si bond necessary for the SiH3 donor. The removalof the t-butyl groups is performed with the reagent2-nitrobenzenesulfenyl chloride in acetic acid at room temperature togive the mixed disulfide. Treatment with LiAlH4 cleaves the S—S bonds togive the free thiols in SSiHD-102, the SiH3DonationS tip, as well assimultaneously reducing the triethoxysilyl group to —SiH3.

FIG. 39 depicts a synthetic pathway for GeH3DonationS. The synthesissteps are as follows: Intermediate SMeD-102X with t-butyl protectedthiols is treated with lithium metal in THF at −78° C. The solution isthen removed by syringe to separate the lithiated germanium species fromthe unreacted lithium metal and then slowly added dropwise to a solutionof PhGeH2Cl at 0° C. to give SGeHD-101 upon workup. This reaction formsthe Ge—Ge bond necessary for the —GeH3 donor. Treatment of SGeHD-101with triflic acid cleaves the Ph-Ge bond to form a Ge—OSO2CF3 bond.Triflic acid also removes of the t-butyl thioether groups. Treatment ofthe this intermediate with LiAlH4 in diethyl ether at 0° C. cleaves anyS—S bonds to give the free thiols in SGeHD-102, the GeH3DonationS tip,as well as simultaneously reducing the Ge triflate group to —GeH3.

FIG. 40 depicts a synthetic pathway for SiMe3DonationS. The synthesissteps are as follows: Intermediate SMeD-102X with t-butyl protectedthiols is treated with lithium metal in THF at −78 C followed by theaddition of chlorotrimethylsilane upon warming to 0° C. Upon workup thecompound SSiMeD-101 with the Ge—Si bond is obtained. The removal of thet-butyl groups is performed with the reagent 2-nitrobenzenesulfenylchloride in acetic acid at room temperature to give the mixed disulfide.Treatment with NaBH4 in chloroform and methanol at room temperaturecleaves the S—S bonds to give the free thiols in SSiMeD-102, theSiMe3DonationS tip.

FIG. 41 depicts a synthetic pathway for GeMe3DonationS. The synthesissteps are as follows: Intermediate SMeD-102X with t-butyl protectedthiols is treated with lithium metal in THF at −78 C. The solution isthen removed by syringe to separate the lithiated germanium species fromthe unreacted lithium metal and then slowly added dropwise to a solutionof chlorotrimethylgermane at 0 C. Upon workup the compound SGeMeD-101with the Ge—Ge bond is obtained. The removal of the t-butyl groups isperformed with the reagent 2-nitrobenzenesulfenyl chloride in aceticacid at room temperature to give the mixed disulfide. Treatment withNaBH4 in chloroform and methanol at room temperature cleaves the S—Sbonds to give the free thiols in SGeMeD-102, the GeMe3DonationS tip.

FIG. 42 depicts a synthetic pathway for intermediate FHD-104X, fromwhich some of the other syntheses begin. The synthesis steps are asfollows: Cis, cis-Tri-O-alkyl 1,3,5-Cyclohexanetricarboxylate is reducedwith lithium aluminum hydride in refluxing THF and vigorous mechanicalstirring to yield cis, cis-1,3,5-tris(hydroxymethyl)cyclohexane HD-1.The procedure used resembles that found in Boudjouk et al.,Organometallics 1983, 2, 336. Cis,cis-1,3,5-Tris(hydroxymethyl)cyclohexane, HD-1, is brominated utilizingtriphenylphosphine dibromide generated in situ. This is accomplished byslow addition of bromine to a solution of the triol andtriphenylphosphine in DMF at room temperature to yield cis,cis-1,3,5-tris(bromomethyl)cyclohexane, HD-2. The procedure usedresembles that found in Boudjouk et al., Organometallics 1983, 2, 336.The tri-Grignard is generated in situ by adding cis,cis-1,3,5-Tris(bromomethyl)cyclohexane, HD-2, at room temperature tomagnesium turnings in THF and heating to reflux. The tri-Grignard isthen transferred to a second reaction vessel to separate the reagentfrom the excess magnesium turnings (Mg is capable of inserting into aGe—Cl bond). Trimethylchlorogermane, previously dried over calciumhydride and degassed, is added slowly dropwise to the reaction at 0 C.After 2 hours, the reaction is warmed to room temperature for two hours,and finally refluxed overnight. The reaction yields predominantly cis,cis-1,3,5-Tris(trimethylgermylmethyl)cyclohexane, HD-3. Cis,cis-1,3-dimethyl-5-(trimethylgermylmethyl)cyclohexane and cis,cis-1-methyl-3,5-bis(trimethylgermylmethyl)cyclohexane are also producedin small amounts. The procedure used is similar to that found inBoudjouk and Kapfer, Journal of Organometallic Chemistry, 1983, 296,339. HD-3 in benzene solution is subjected to redistribution reactionconditions using high purity anhydrous aluminum trichloride and heatingto reflux to yield 1-methyl-1-germaadamantane. HD-3 side products cis,cis-1,3-dimethyl-5-(trimethylgermylmethyl)cyclohexane and cis,cis-1-methyl-3,5-bis(trimethylgermylmethyl)cyclohexane may also bepresent in the reaction or isolated and reacted under these conditionsto yield HD-4 as well. HD-4 is reacted with excess “ketone free”dimethyldioxirane (DMDO) (Crandall, J. K. 2005. Dimethyldioxirane.e-EROS Encyclopedia of Reagents for Organic Synthesis.) in methylenechloride solution at −20 C to yield1-methyl-3,5,7-trihydroxy-1-germaadamantane RHD-101. The absence ofacetone in the reaction conditions allows for RHD-101 to precipitatefrom the reaction mixture, preventing over-oxidation. Upon completion ofthe reaction, isopropyl alcohol is used to quench the excess DMDO,preventing over-oxidation by excess reagent during reaction workup.RHD-101 is subjected to strongly acidic conditions in the presence of2,4,6-trifluorophenol at room temperature to yield FHD-102. The use ofBrønsted acidic conditions favors carbocation formation at the 3,5,7bridgehead positions of the adamantane cage structure overredistribution reactivity at the germanium center. The 1-methyl group ofFHD-102 can be exchanged with a halide (X=F, Cl, Br, I) with a varietyof electrophilic reagents at low temperatures ranging from −78 C up toroom temperature, depending on the halide desired. Reagents include, butare not limited to: Lewis acids such as SnCl4 or GaCl3, elementalhalides Br2 and 12 with Lewis acid catalyst, alkyl halides such asisopropyl chloride with Lewis acid catalyst, and interhalogen compoundssuch as IBr and ICl. Furthermore, heavier FHD-103X halides can beconverted to lighter halides utilizing the appropriate lighter silverhalide (e.g. FHD-103Br and AgCl will produce FHD-103C1). The phenolicalcohols of FHD-103X (X=F, Cl, Br, I) can be protected utilizingtert-butyl(chloro)diphenysilane and imidazole in DMF at RT to yieldFHD-104X (X=F, Cl, Br, I).

FIG. 43 depicts a synthetic pathway for intermediate NHD-103X, fromwhich some of the other syntheses begin. The synthesis steps are asfollows: RHD-101 is subjected to strongly acidic conditions such asmethanesulfonic acid in the presence of 2,4,6-trifluoroaniline at roomtemperature to yield NHD-102. The use of Brønsted acidic conditionsfavors carbocation formation at the 3,5,7 bridgehead positions of theadamantane cage structure over redistribution reactivity at thegermanium center. To form NHD-103, NHD-102 is alkylated at roomtemperature with 4-methoxybenzyl bromide in DMF with potassium carbonatebase in the presence of potassium iodide. To form NHD-103X, the 1-methylgroup of NHD-103 can be exchanged with a halide (X=F, Cl, Br, I) with avariety of electrophilic reagents at low temperatures ranging from −78 Cup to room temperature depending on the halide desired. Reagentsinclude, but are not limited to: Lewis acids such as SnCl4 or GaCl3,elemental halides Br2 and 12 with Lewis acid catalyst, alkyl halidessuch as isopropyl chloride with Lewis acid catalyst, and interhalogencompounds such as IBr and ICl. Furthermore, heavier NHD-103X halides canbe converted to lighter halides utilizing the appropriate lighter silverhalide (e.g. NHD-103Br and AgCl will produce NHD-103C1).

Surface Preparation

Two exemplary surfaces are described herein, silicon and gold. Morespecifically, partially-hydrogenated partially-chlorinated Si(111), andatomically-flat Au(111).

Partially-hydrogenated partially-chlorinated Si(111) reduces the energybarrier to the tip molecules binding as compared to just chlorinatedSi(111) because the hydrogen, being smaller in size than Cl, helpsreduce steric congestion as the tip approaches the surface.Hydrogenation is preferably in the 33%-50% range, although wider rangeswill work, as will not using hydrogenation at all. Partiallyhydrogenated partially-chlorinated Si(111) can be prepared in a numberof ways. One is the following.

Clean, atomically flat doped Si(111) surfaces are prepared by directcurrent annealing the Si for several hours at ˜650C followed by rapidheating to ˜1200C for 1-20 sec while keeping the chamber pressure<1×10-9 Torr. This procedure gives the 7×7 reconstructed Si(111)surface, as in J Phys Cond Matt 26, 394001 (2014).

The Si(111) surface can be chlorinated by depositing C12 from anelectrochemical cell similar to the one in J Vac Sci and Tech A 1, 1554(1983), while the Si(111) is heated to ˜400C. Atomically flathalogenated Si(111) surfaces have been prepared this way, as in Phys RevLett 78, 98 (1997).

Si(111)-Cl surfaces can then be partially hydrogenated by exposing thesurface to 600 L of atomic hydrogen from a H2 cracker, as in Surf Sci402-404, 170-173 (1998), with the Si(111)-Cl at room temperature.

Clean, atomically flat Au(111) surfaces are prepared by repeated cyclesof sputtering and annealing a single crystal Au(111) surface, as in PhysRev Lett 80, 1469 (1998).

Tip Bonding

Once synthesized, a tip can be bound to a presentation surface, ameta-tip surface, or a single-tip tool surface. Many ways of bindingtips to surfaces are possible, and these may vary with the exact natureof the tip and the surface.

One method of depositing isolated tips on a surface is via thermalevaporation in vacuum. In this technique, purified molecules in the formof a solid or liquid are heated up in a vacuum chamber until theyevaporate as a gas of isolated molecules. By placing the presentationsurface within this gas, individual tips will adhere to the surfaced.(See tetramantane deposition in Nature Materials 7, 38 (2008)). Thismethod has the advantage of depositing molecules without surfacecontamination from a solvent and can be used with masks to pattern asurface.

The tips having sulfur or thiol-based linkers will bond to goldspontaneously at room temperature. The tips with 0 or NH linkersdesigned to bond to chlorinated silicon surfaces require heating of thesurface to overcome reaction barriers (hence the partial hydrogenationbeing favored as it keeps the activation barrier as far below the tipdecomposition temperature as possible).

A simple way to evaporate molecules is to place the molecules in a glassor alumina crucible with a tungsten wire wrapped around the crucible.Passing a current through the wire heats the crucible and molecules,generating a molecular gas that exits the front of the crucible. Athermocouple on the crucible measures its temperature. A quartz crystalmicrobalance can be used to determine how much is evaporating as afunction of time and temperature.

This is just one example of how tips could be bonded to a surface. Suchtechniques, including how to create sectors of specific molecules, arewell-known in the respective arts. (Zahl, Bammerlin et al., “All-in-onestatic and dynamic nanostencil atomic force microscopy/scanningtunneling microscopy system,” Review of Scientific Instruments, 2, 2005;Sidler, Cvetkovic et al., “Organic thin film transistors on flexiblepolyimide substrates fabricated by full-wafer stencil lithography,”Sensors and Actuators A: Physical, 2, 2010; Vazquez-Mena, Gross et al.,“Resistless nanofabrication by stencil lithography: A review,”Microelectronic Engineering, 2015; Yesilkoy, Flauraud et al., “3Dnanostructures fabricated by advanced stencil lithography,” Nanoscale,9, 2016)

Tip Activation

Tips, particularly those with exposed radicals at their active site, maybe bonded to a surface in an inactive form. One method of activatingsuch tips is through photo-cleavage of the structure. For example, thehalogen-capped tip examples herein can be activated through exposure to254 nm light. FIG. 44 depicts an activating reaction for halogen-cappedtips. Other wavelengths and chemistries can be used. For example, ifdifferent synthetic steps were used, a tip could be protected with aBarton ester, which can then be cleaved, activating the tip, with 365 nmlight. FIG. 45 provides an example of the activation reaction that couldbe used with a Barton ester.

While not the only way to remove a tip cap, photo-activation isconvenient in that different areas of a surface can be masked, orexposed to different wavelengths, making this a versatile technique evenwhen multiple types of tips are desired on a single surface.

Barton Ester Caps

Other examples are provided herein of synthetic routes to halogen-cappedtips, and how to activate them. To demonstrate another chemistry forsynthesizing tips with protective caps, the Barton ester is analternative that fragments upon being irradiated with, for example,355-365 nm wavelength light to give the carbon centered radical, CO2,and the pyrithiyl radical. (Barton, D. H. R., Crich, D., Potier, P.Tetrahedron Lett., 1985, 26, 5943-5946. For a review of thiohydroxamicacids chemistry see: Crich, D., Quintero, L. Chem. Rev. 1989, 89,1413-1432) These types of activated molecules can be made from thedescribed compounds and one such synthetic route is described below,resulting in the Barton ester version of the AbstractionO tip.

FIG. 46 depicts the synthesis of the Barton ester AbstractionO tip,which is as follows: To synthesize the Barton ester for photoactivation,propynoic acid OFAB-1 is made from OFA-7 using the traditionalCorey-Fuchs procedure and quenching by bubbling gaseous CO2 through thereaction mixture. (Corey, E. J., Fuchs, P. L. Tetrahedron Lett. 1972,36, 3769-3772) The first step forms the 1,1-dibromoalkene in solution at−78 C. The addition of 2 more equivalents of butyllithium forms thelithium acetylide in the reaction mixture. By bubbling with the carbondioxide the desired carboxylic acid OFAB-1 is obtained after an aqueousworkup. To make the Barton ester, carboxylic acid derivative OFAB-1 isactivated to the acid halide by oxalic acid and catalyticN,N-dimethylformamide (DMF) in dichloromethane at room temperature. Tothis reaction mixture the sodium pyrithione salt is added to the mixtureto form the desired ester bond in compound OFAB-2. The Barton ester isunstable to aqueous acidic and basic media, so careful control ofreaction conditions must be taken when removing the protective groups.Multiple techniques are possible for removal of silyl ethers such asOFAB-2 that are pH sensitive. One is to use more labile silyl etherssuch as trimethylsilyl- (TMS-) or triethylsilyl- (TES-) ethers in placeof the more stable TBS silyl ethers. Another method is to use OFAB-2 andcatalytic solid tetra-n-butylammonium fluoride (TBAF) or cesium fluoridein 100:1 THF-buffer solution to produce OFAB-3. A solution of K2HPO4buffered at pH=7.1 could be used in the TBAF deprotection. (DiLauro, A.M.; Seo, W.; Phillips, S. T., J. Org. Chem. 2011, 76, 7352-7358) Thisdecreases the risk of hydrolyzing the Barton ester bond and increasesthe likelihood of obtaining the free phenols in OFAB-3, the Barton esterAbstractionO tip.

Using Tips

One of the ways in which surface mounted tips can be used is depicted inFIG. 47. This figure is diagrammatic and not to scale. In FIG. 47,handle 4701 is connected to surface 4702. Surface 4702 is optional,serving to provide the desired materials and chemistry to bind workpiece4703 in the case where the material of the handle is unsuitable fordoing this directly. It is possible to bind workpiece 4703 directly tohandle 4701. Handle 4701 would be connected to a positional means (notshown) for the purposes of moving handle 4701, and thereby workpiece4703 with respect to tips (of which tip 4704 is representative) mountedon surface 4705.

In the depicted position, workpiece 4703 could be descending upon a tip,or it could be rising from just having used a tip. Regardless, the pointis that surface 4705 can contain many tips, of many different types,including non-functional tips (which either failed to synthesizecorrectly or have already been used). Knowledge of tip position, forexample, because sectoring was used to place certain tip types incertain locations, or via scanning the surface (before or during a buildsequence), allows the workpiece to be moved to a desired tip, at whichtime a mechanosynthetic reaction occurs, and the workpiece then moves tothe next desired tip. This process is repeated until the workpiece iscomplete.

Another way to use surface-mounted tips is to create a meta-tip, whichis a handle upon which a plurality of tips may be mounted, directly, orvia a surface. FIG. 48 depicts this mode of using surface-mounted tips,where handle 4801 is connected to (optional) surface 4802. Handle 4801is also connected to a positional means (not shown). Tips, of which tip4804 is representative, are shown mounted on surface 4802, but could bemounted directly to handle 4801. In this scenario, the tips move to actupon workpiece 4803, which resides upon surface 4805.

The main difference between the scenarios of FIG. 47 and FIG. 48 iswhether the workpiece moves or the tips move. In actuality, it ispossible that both move (e.g., one for course adjustments, one forfine), and the distinction is mainly one of equipment design.

FIG. 48 perhaps provides the clearest illustration of the advantagessurface-mounted tips have over previous mechanosynthesis techniques. Ifsurface 4802 only had one tip affixed to it, it would be analogous tothe tips commonly used for mechanosynthesis. In this scenarios, it isobvious that to create complex workpieces, the affixed tip would have toa) be capable of multiple reactions and b) be regenerated frequently,or, the affixed tip would have to be frequently swapped to connect othertips to the positional means (not shown). Using either the scenario ofFIG. 47 or FIG. 48 (and modifications thereof which would be obviousgiven the teachings herein), many tips are available to providemechanosynthetic reactions, potentially (depending on the number of tipsinitially available and the number of reactions required to build theworkpiece) without tip recharge and without tip swapping. Any reductionin tip recharge or tip swapping can help decrease the average time ittakes to perform a reaction.

Note that surface-mounted tips could be used to build otheratomically-precise tips, including building them directly onto the endof a handle or probe. This is another manner in which surface-mountedtips could be used to avoid a bootstrap sequence that usesnon-atomically-precise tips.

Mechanosynthesis-Adapted Equipment

Efficient mechanosynthesis has a different set of requirements thantypical SPM work. Typical SPM work involves analysis rather thanmanufacture, the point generally being to scan specimens to create animage or collect other data. Scan speed is frequently the limitingfactor, and increasing scan speed is an active area of research (Dai,Zhu et al., “High-speed metrological large range AFM,” MeasurementScience and Technology, 9, 2015).

Scan speed is less important to systems for mechanosynthesis as long asthe system can obtain the necessary accuracy without scanning. Ideally,other than perhaps scanning the surface initially to locate and identifytips, and perhaps scans of very small areas to check that a reactionoccurred correctly, systems adapted for mechanosynthesis would not needto scan. Doing away with scanning for position refinement, and insteadusing metrology that allows the requisite point-to-point accuracy(meaning, moving directly from one tip or workpiece location to another,without using scanning in between to refine position), wouldconsiderably speed up the process of mechanosynthesis.

Note that while the ideal attributes for analytical or metrological SPMare different than those for systems for mechanosynthesis, even previouswork on mechanosynthesis did not provide systems well-adapted for suchwork, due to the simple and low-volume nature of the work beingperformed.

Other useful adaptations that are somewhat unique to the requirements ofmechanosynthesis include reducing tip recharge and reducing tip swapping(which does occur in more conventional uses of SPM equipment, butfrequently because a tip has been damaged, not because many tips ofdifferent chemical natures are required, making the required frequencyof tip swapping quite different). Surface mounted tips have beendiscussed herein as one way to reduce the need for tip recharge and tipswapping.

With respect to obtaining the necessary point-to-point accuracy (ideallysub-Angstrom, although less accuracy could be coupled with scanning ofvery small areas to precisely localize the tip), positional meanscapable of very high accuracy of large distances are available. Forexample, using Fabry-Perot interferometry, picometer-level accuracy hasbeen shown to be possible at distances of 50 mm. (Lawall, “Fabry-Perotmetrology for displacements up to 50 mm,” J. Opt. Soc. Am. A, 12, OSA,2005)

However, since mechanosynthetic reactions are generally not occurringexactly at the point being measured (which is generally, e.g., areflective flat when using laser interferometry), such metrology stillhas to be carefully implemented to avoid, e.g., Abbe error which can beinduced by slightly non-linear movement of the tip or workpiece withrespect to, e.g., the reflective flat. One way to address this issue itto measure not only the X, Y and Z coordinates of the reflective flat,but also to measure (and so be able to account for) any rotation thatmight be occurring around these axis as well.

One way to measure both linear and angular position is to use 6interferometers (e.g., Michelson or Fabry-Perot opticalinterferometers). FIG. 49 illustrates one way interferometers can beused to measure six degrees of freedom (X, Y, and Z, and rotation abouteach of those axes).

In FIG. 49, Reflective mirrors 4901-4906 and, and their respectivebeams, BeamZ1 4907, BeamZ2 4908, BeamZ3 4909, BeamX1 4910, BeamY1 4911and Beam Y2 4912 can be used together to determine position in all sixdegrees or freedom. The spacing between various pairs of beams must beknown to compute rotations. In this scenario, BeamX1 provides the Xposition. BeamY1 or BeamY2 provide the Y position. BeamZ1, or BeamZ2, orBeamZ3 provides the Z position. BeamZ1 and BeamZ2, together with thedistance between the two beams allows the rotation about the X axis tobe calculated. BeamZ2 and BeamZ3, together with the distance between thetwo beams allows the rotation about the Y axis to be calculated. And,BeamY1 and BeamY2, together with the distance between the two beamsallows the rotation about the Z axis to be calculated.

Coupling the ability to provide, ideally, sub-Angstrom linear distancemeasurement over millimeter distances, while also measuring andaccounting for angular errors, with, for example, a microscope thatoperates at 4K (room temperature is feasible but more technicallychallenging) in ultra-high vacuum, using a qPlus sensor, provides for asystem that can access precise locations on large presentation surfaceswith a greatly-reduced need to use scanning and image recognition torefine the relative position of a tip and the workpiece. Theseadaptations themselves are valuable for mechanosynthesis. Using suchequipment with surface-mounted tips and the processes described hereinprovides systems adapted for mechanosynthesis that can provide muchgreater reaction throughput than conventional systems.

What is claimed is:
 1. A tip, comprising: an adamantane body substitutedwith Ge at a bridgehead position; wherein said Ge constitutes an activesite having feedstock bound thereto, said feedstock being selected fromthe group of, CH₂ radical, SiH₃, GeH₃, SiMe₃, and GeMe₃, and one or morelegs, connected to said adamantane body at one or more positions whichallow other tips or workpieces access to said active site for thepurposes of carrying out a mechanosynthetic reaction.
 2. The tip ofclaim 1 wherein said feedstock bound to said active site is CH₂ radical.3. The tip of claim 1 further comprising SiH3 wherein said feedstockbound to said active site comprises SiH₃.
 4. The tip of claim 1 whereinsaid feedstock bound to said active site comprises GeH₃.
 5. The tip ofclaim 1 wherein said feedstock bound to said active site comprisesSiMe₃.
 6. The tip of claim 1 wherein said feedstock bound to said activesite comprises GeMe₃.